Eleven Australians took part in the Global Sumud Flotilla to Gaza in May when they were detained in international waters at gunpoint, before being imprisoned and eventually deported from Israel.
Members of the group allege they experienced violence, sexual assault and abuse while in the custody of the Israelis.
Australian Federal Police have begun inquiries into the allegations.
But Israel's ambassador to Australia Hillel Newman said he had not seen any request from federal police.
"They're wasting their time on such a futile accusation of such kind," he told ABC radio on Wednesday.
"We respect the AFP. If this is a professional examination, I'm sure we will co-operate. If this a witch hunt and trying to support a wild accusations, then I'm not sure how we will respond to it."
Members of the flotilla met with Foreign Minister Penny Wong and AFP representatives at Parliament House on Monday.
Senator Wong has previously told parliamentary hearings she believed the testimonies of the Australian activists.
Mr Newman rejected the allegations of the flotilla members, saying there was no evidence to support their claims.
"These people are not random, innocent people. These are professional provocateurs," he said.
"You can't wake up any morning and be accused of rape, and then you have to go and prove that you didn't do it.
"We respect the AFP, but you cannot prove a negative, you cannot prove that you didn't."
Neve O'Connor, who participated in the flotilla, said the group wanted to see "strong accountability".
"We would like to see a government that acts on behalf of their Australian citizens who have been abused, tortured, and raped, and actually act on our benefits," she told reporters on Monday.
Israel's National Security Minister Itamar Ben-Gvir attracted global condemnation after he posted a video of himself taunting detained activists as they knelt on the ground with their hands zip-tied behind their backs.
